chr13-31715910-G-A

Variant names:

• chr13-31715910-G-A
• rs1887570

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.627 in 151,954 control chromosomes in the GnomAD database, including 34,457 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.63 (34457 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95210 AN: 151836 Hom.: 34456 Cov.: 31

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.749

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.746

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.637

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.666

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.627 AC: 95230 AN: 151954 Hom.: 34457 Cov.: 31 AF XY: 0.629 AC XY: 46712 AN XY: 74276

African (AFR) AF: 0.245 AC: 10153 AN: 41466

American (AMR) AF: 0.735 AC: 11220 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.749 AC: 2598 AN: 3468

East Asian (EAS) AF: 0.520 AC: 2682 AN: 5160

South Asian (SAS) AF: 0.748 AC: 3591 AN: 4804

European-Finnish (FIN) AF: 0.772 AC: 8139 AN: 10548

Middle Eastern (MID) AF: 0.627 AC: 183 AN: 292

European-Non Finnish (NFE) AF: 0.803 AC: 54564 AN: 67936

Other (OTH) AF: 0.662 AC: 1399 AN: 2112

Alfa AF: 0.703 Hom.: 5065

Bravo AF: 0.602

Asia WGS AF: 0.610 AC: 2125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
DANN	Benign	0.55
PhyloP100		0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1887570; hg19: chr13-32290047;